The Weapon Within
by Denaliyasha
Summary: Long ago, the Ancients seeded the human race with a gene that, when combined with the Ancient gene, produced a living weapon of unimaginable power. One of the Atlantis team is about to undergo gene therapy.
1. Chapter 1

Disclaimer: None of the characters are mine.

A/N: This was a LONG time coming. :D If it weren't for my wonderful beta Atlantisfan101 and the contributions of many other people (including my mother, who doesn't even really like fanfiction), I've actually got a full plot BEFORE I start a big story. And they're going to harass me till I post, so you don't have to worry TOO much about me going years without the next chapter. That said, my life is really, really stressful right now. Therefore, it might not be as fast as you want it to be, and bugging me about it in your reviews will not do you any good.

Anyone who's both read my fanfic Fitting (Stargate SG-1) and seen the Stargate SG-1 episode 200 will totally know that I called the wedding scene. You can find it on youtube .com... She calls him Sir, he calls her Carter. I rest my case.

**The Weapon Within**

"Colonel Sheppard! Colonel Sheppard!" Rodney's voice carried down the long hallway, and, because John couldn't think of an excuse not to stop, he turned and waited for the scientist to catch up with him.

"Yes?"

"Have you seen Elizabeth? She has to see this." John had to lean back to avoid the laptop being brandished in his face by the excited scientist. "She really has to."

"She's getting the ATA gene therapy this afternoon, I think. She's probably in the infirmary." He checked Rodney's rush in that direction with a firm hand on the shoulder. "I'll walk with you, and you can tell me about it on the way."

"Fine, fine." Rodney made an exaggerated show of waiting for John to start walking before he started talking a mile a minute.

"So I was searching through some of the Ancient database, and I found the mention of a gene."

"The ancient gene."

"No." Rodney smiled smugly. "Another gene. They called it the Atlantis gene, and it developed by them instead of just passed down. They knew that the one day they might come up against an enemy that they couldn't face and they couldn't run from, so they created this gene. It's designed to work with the Ancient gene; I suppose they thought they'd use it on themselves, if necessary. When one person has both of the genes, they become sort of a..." He waved his hand around, searching for the right phrase. "Super Ancient. It didn't give specifics, but it seems to be things like controlling the technology with their minds, and being closely in tune with everything the Ancients built."

"So what's so urgent?" It was exciting, sure, but nothing that needed immediate attention.

"The Ancients didn't want to leave humans without defenses, so they seeded the human race with the Atlantis gene when they ascended. So..." He trailed off, looking expectantly at John.

"So if we can find a person with this gene, we can give them the ATA therapy and we'll have a valuable weapon against the wraith."

"Exactly. The gene is really, really rare, though. Still, maybe one person on Atlantis has it."

John grinned. "You have a point. To the infirmary, then."

Neither of them said anything as they speed-walked (because they had some sense of dignity left, and besides, if they'd run, people would have panicked) to the infirmary. As Rodney rushed through the door, John called, "If she's still tired, this can wait until after we see if the gene took, ok?"

And then he almost ran into the hyper-active scientist, who'd stopped dead just inside the room. "Oh, it took alright." John followed his gaze to the bed where Elizabeth was lying... and realized why Rodney had stopped.

She was leaning back against the pillows, eyes closed as though in a brief nap. From the inside corners of her eyes seemed to be sliding navy dye, running in a line down her cheeks like the tear markings of a cheetah.

"What the hell?" John started to make his way across the room, only to be stopped by Rodney's hand on his arm.

"That's... that's..."

"What is it, Rodney?" He had a sneaking feeling that he wasn't going to like what he was about to hear.

"Oh, the Ancient gene definitely took. Colonel, that's the marking from the database."

"What?" He was putting two and two together and getting four, but he wasn't sure he liked that number.

"The one from the file on the Atlantis gene. She must have had it, and the therapy..."

"Turned her into a super-Ancient." John turned to stare at the commander of the expedition, the woman he'd grown to respect and care for over the course of their time there. "Oh boy."

As though she felt his stare, her eyes slid open, and their color had deepened to a dark, cobalt blue. "John? Did you need something?"

A/N: Muah... semi-cliffy


	2. Chapter 2

Disclaimer: See first chapter.

A/N: I have to say, I have no respect for people who leave anonymous reviews saying nothing but, "You need to update! Don't leave us hanging!" I believe I made it clear at the beginning that my life is the most hectic it has ever been. I try, but I don't have that much time and this story takes more concentration than one-shots like those I've been posting. If I were to rush this, how well written do you think it would be?

Thanks to all my honest reviewers, and I'm sorry I made you wait this long.

**The Weapon Within**

"You're... you're..." Rodney couldn't seem to say anything coherent, sputtering and choking on his words.

"Rodney?" Elizabeth shifted her gaze to him, puzzled. "What's the matter?"

"I... You..." He was staring, wide-eyed, at her face.

"John? What's wrong with Rodney?"

John, who'd been basking in the idea of a speechless Rodney, sighed. "He's freaking out because..."

"Because you're it! You've got it! You're..." Rodney's voice had risen to a yell, and before John could get on him for interrupting, his earpiece crackled into life.

_"Sir? Whatever Doctor McKay is doing, you need to tell him to hold still."_

"Why?"

_"Because all of Atlantis' internal defense systems just came online, including some weapons we didn't know about, and it's locked onto him."_

"Rodney." The babbling continued. "RODNEY!" Rodney stopped talking and turned to face him. "You need to calm down and stop moving and talking. Atlantis has apparantly decided you're some kind of threat, and every weapon in the place is pointed at you. You make one wrong move, and you'll be atoms."

There was silence for a moment, then, "Well, technically I already am..."

"RODNEY!"

"John, what is going on?" Elizabeth was looking back and forth between the two men, concern in her now blue eyes.

To make matters worse, Carson chose that moment to pop out of the woodwork. "What's this?"

"Ok, I'm going to explain as best I can, but first, Elizabeth..." John moved carefully to stand next to her bed and put a hand on her arm. "It's important that you calm down, so that you don't kill Rodney before I'm through."

She closed her eyes, and he could see her reaching for her famous diplomatic calm. When she opened them again, he was distracted by the fact that they were once again green and almost missed the fact that she was speaking. "Tell me, John."

"Rodney found the mention of a gene in the Database. It was designed by the Ancients to combine with the Ancient Gene to produce a kind of super soldier to fight the wraith. They scattered it in the human race when they left Earth."

"And?" Her eyebrow went up, and he could see little slivers of cobalt bleeding into her irises.

"And... the sign that the two genes are active in a person are marks dyed onto the face, apparantly."

"What does that have to do with me?" The blue was overwhelming the green, and he hurriedly reached for a nearby polished silver tray. Figuring that she'd need to see it to believe it, he held it up so she could see her reflection.

"Oh my God..." Her eyes drained suddenly back to their natural color as her face turned completely white.

There was a few moments of silence, then Rodney said, "Do you think you could call off the attack on me now?"

A/N: This is unbeta-ed in an effort to get it out sooner. Sorry, I'll try to do better next time.


	3. Chapter 3

Disclaimer: See first chapter.

A/N: Sorry about the wait. Again, unbeta-ed to get it to you faster. Inspired by watching Sparky music videos. On that note, if anyone has clips of Sparky moments they wouldn't mind sharing, send me a PM. I would totally love you forever and write you into a story... :)

**Chapter Three**

Twenty minutes later, Carson, John, and Rodney were waiting for Elizabeth to come out of the bathroom. She'd asked for a few minutes to pull herself together, and, mindful of what had almost happened to Rodney, they'd put up no protests.

That had been fifteen minutes ago.

Rodney had gotten out his laptop and was explaining to Carson exactly what the Atlantis gene was. John was pacing in front of the bathroom door. He was the only one to hear the heavy sigh right before the door opened.

"Rodney?"

"Yes?" He spun on his heel and cringed slightly. Only John was close enough to see the hurt flicker through Elizabeth's eyes in a wave of blue. He turned to ask Rodney to leave the room, but she beat him to it.

"Rodney, I need you to leave."

"Why?" He looked like someone had just snatched his favorite toy.

"Anything that irritates me in the slightest is obviously in danger at the moment. You have an... abrasive personality. Until I learn to control this, I have to ask you to stay away from me for your own safety."

"But..."

"That's an order, Rodney." John stepped in before Rodney could say anything stupid. "Leave. I'll come find you later and get details about the gene."

"Alright." Rodney was pouting. "But if annoying is the problem, why aren't you leaving?"

"Because he's the only one here who I trust right now, damn it!" All attention focused back on Elizabeth. She was obviously struggling for control, eyes closed and hands fisted. "I need someone that I know will tell me the truth without prejudice or shading, and I need someone I know will do what has to be done without hesitation. That is not you, Rodney, nor is it you, Carson."

"I think I need to be here, though." The doctor stepped cautiously towards her.

She nodded. "Yes. But I need for Rodney to leave, and I need for John to stay. Otherwise, I'm going to lose my temper and I'm going to hurt someone and I can't live with that." She forced her eyes open; they were shot through with blue. "Please, Rodney, do me this favor."

"Leaving!" He practically sprinted from the infirmary.

"Alright. What are the implications of this on my ability to do my job?"

The two men looked at each other, and in that glance decided that John was going to do most of the talking. "As far as I can tell, this just makes you better for the position. You can control Atlantis with a thought... that means if you need to put it on lockdown or quarantine a section, you can do that. However, it also makes you a liability if you ever leave the city. By manipulation of you or your mind, which we've already got proof some that some of our enemies can do, they would have total control over the city."

As he spoke, Elizabeth began pacing, unknowingly taking the same path he had earlier. "And the medical implications?"

"From what Rodney told me, you're better than ever. Apparently, you'll need to sleep even less, eat less. You'll be able to draw energy directly from the city and Ancient technology. You're more resilient than you were. I think that's it."

"So, I don't get to fly or anything?" Her mouth twisted in a smile, and the blue markings on her face warped slightly.

"Sorry. Though I think you could still wear the Wonder woman costume if you wanted." John flashed a cheeky grin at her, and she laughed... then started crying. Stepping up so that he blocked Carson's view of her, John gently wrapped his arms around her. "It's going to be fine, Elizabeth. I promise, we'll figure this out."

A/N: Needed to get this all out. Sorry it's lacking in as much humor and Sparky-ness. The next chapter will be most definitely very Sparky.


	4. Chapter 4

Disclaimer: See first chapter.

A/N: Sorry for the delay. And to Brittany, sorry it's taking so long, yes, I will be finishing this story. Preferably before I die, but who knows? Maybe I'll be a ghost writer... :) Also, seriously, I found a great song for a music vid... if you have clips I could use, I'd love you forever. And maybe make you a character in this story?

**Chapter Four**

She very deliberately didn't look up from her paperwork when she heard him come in. If she looked, she knew she'd be blushing.

"Elizabeth, we need to work on this."

Reluctantly, she dragged her eyes up. This had the unfortunate affect of giving her a great view of the uniform covering the chest she'd recently seen bare... It took huge effort not to just stare... and stare, and stare... "I'm sorry?" She finally made the visual journey to his face.

"We need to work on the fact that apparently, needing me to sign a report is enough of a need that Atlantis will let you into my quarters." He folded his arms over his chest, looking more amused than he had any right to, considering what had been going on less than an hour ago...

_"John? Are you..." She trailed off as the door to his room slid open without warning. Instead of her military commander standing in the doorway, however, he was across the room... wearing nothing but a towel wrapped around his waist._

_As he turned, the only thought she could form was, dear God, he was built. And he was just as hot as she'd thought he would be._

_"Elizabeth? What are you doing in my room?"_

_"Um..." She couldn't seem to form coherent thought. "I had a mission report for you to sign off on... I needed..." She didn't let herself finish that particular sentence. She had a feeling she would regret whatever she might have said._

_"Uh, ok, can it wait till I'm a little more dressed?" He planted his hands on his hips, making his chest flex, and she was lost._

_"Yes! Definitely!" She turned and ran for the safety of her office, uncaring of how she must look to the citizens of Atlantis._

"Well, what would you suggest?" Elizabeth realized she sounded defensive, but she didn't care.

"I suggest that you practice. Concentrate on the door, not what you need from whoever's inside. That way, Atlantis knows it's not vital and you knock, instead of breaking the door down. Metaphorically, of course."

"I'll do my best, in the future."

"Good. I'm not a prude, but having a woman walk in unexpectedly while I'm half naked usually only happens when I drank a hell of a lot the night before." He flashed that smile, and it took her brain with it.

"Well, then a lot of women don't know what they're missing..." She clapped a hand over her mouth, shocked at herself. She could practically feel the heat creeping up her cheeks, accenting the dark marks the Atlantis gene had tattooed on her face.

"Elizabeth!" There was genuine shock in his voice, which turned into teasing quickly as he took the few steps needed to have him standing right in front of her desk. "Are you saying you liked the view?"

"No?" She could tell he didn't believe her. Hell, she didn't believe herself.

"Really..."

Fighting fire with fire seemed to be the only method. "John, you know you're the sexiest man in the city. You're our answer to Captain Kirk. You honestly expected me not to like what I saw?"

He just stared at her blankly for a few seconds. "I'll have you know those rumors are totally overrated."

"Yeah, right, John. I read the mission reports."

Obviously desperate to change the subject, he said, "Didn't you have something you needed me to sign?"

"Here." She passed it across to him, and he sat down to scribble his name across the bottom. How he read his own handwriting, she wasn't sure. It was horrible. "Thank you."

"You gonna get food any time soon?"

She checked her watch, which Rodney'd managed to set up to Atlantian time. It was nearly lunch. "Probably."

"Mmm." He stood, moving to the door. He paused, half turning to her. "Do you want to get it with me?"

"If you're willing to wait a few minutes." She went back to her paperwork.

"That's not what I meant. I meant, did you want to get food with me. Have a meal with me. Like a date."

A/N: Sorry for the cliffy. I couldn't figure out how to end it otherwise.


End file.
